Design of Custom Expression Microarrays in the Post-ENCODE Era
Arnold C, Externbrink F, Hackermüller J, Reiche K. 2013. Design of Custom Expression Microarrays in the Post-ENCODE Era. Journal of Biotechnology 189:154-156. [PDF]
Microarrays are widely used in gene expression studies, and custom expression microarrays are popular
to monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomes
uncovered recently make custom expression microarray design a non-trivial task. Pervasive
transcription and alternative processing of transcripts generate a wealth of interweaved transcripts that
requires well-considered probe design strategies and is largely neglected in existing approaches.
We developed the web server CEM-Designer that facilitates microarray platform independent design
of custom expression microarrays for complex transcriptomes. CEM-Designer covers (i) the collection
and generation of a set of unique target sequences from different sources and (ii) the selection of a set of
sensitive and specific probes that optimally represents the target sequences. Probe design itself is left to
third party software to ensure that probes meet provider-specific constraints.
CEM-Designer is available at http://designpipeline.bioinf.uni-leipzig.de.